Bwa: Number Of Threads

Question

[Pierre Lindenbaum]

OK, I'm really not a hardware-guy: I want to run bwa and here is a snapshot of my /proc/cpuinfo

#grep "physical id" /proc/cpuinfo | sort | uniq | wc -l
4
#grep ^processor /proc/cpuinfo | wc -l
16
#grep 'cpu cores' /proc/cpuinfo | sort | uniq
cpu cores    : 4

what would you suggest as a good value for the number of threads to be used by bwa (option -t ) ?

Thank you ! :-)

Answer 1

[Aaron Statham]

Looks to me like you have 4xquad core CPUs - I would use 15 threads, that way you still have one core free to do other things in the meantime

[Stefano Berri]

Agreed. You could also use nice and use all processors:

nice -19 bwa -t 16 ...